I can not get a decent timer to work for capturing Minecraft gameplay as the mods will not work. I can though get an obs timer to record but only in increments of seconds and it would constantly count down. Is this ok or does it have to be a in-game timer capturing all the way down to milliseconds?

1. Ask the mods of the game if you have concerns about whether something would be allowed.
2. Ask the mods/community of the game for help if you're having difficulty setting up any of their resources.
3. Any timer should work, even something like Livesplit is very easy to setup and have it count upwards. You can find all sorts of timers on http://www.speedrun.com/resources